Contacts of the helix formed by residues 71 - 79 (chain C) in PDB entry 3NA0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 71 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A GLN* 4.0 20.0 - - - +
50C LEU* 4.2 9.1 - - + +
72C ASP* 1.3 64.5 + - - +
73C GLU* 3.6 15.5 + - - +
74C GLU* 3.1 43.5 + - - +
75C ASN* 3.2 26.7 + - - +
93C GLN* 5.9 4.0 - - + +
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Residues in contact with ASP 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A LEU 3.5 4.0 - - - +
372A GLN* 3.1 35.7 + - - +
375A PRO* 5.1 12.9 - - - +
378A LYS* 3.3 33.1 - - + +
71C THR* 1.3 75.3 - - - +
73C GLU* 1.3 72.2 + - - +
75C ASN* 3.3 19.2 + - - +
76C ASP* 3.0 26.0 - - - +
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Residues in contact with GLU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A GLN* 4.3 7.9 - - - +
378A LYS* 3.5 24.6 + - - +
466A ARG* 3.7 39.2 + - - +
469A GLU* 4.4 6.9 - - - +
470A LEU* 6.0 3.2 - - - +
50C LEU* 4.1 17.2 - - + +
71C THR* 3.3 16.2 - - - +
72C ASP* 1.3 82.0 + - - +
74C GLU* 1.3 65.1 + - - +
76C ASP* 3.4 12.6 + - - +
77C MET* 3.3 27.2 + - - +
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Residues in contact with GLU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 4.2 7.3 - - + +
71C THR* 3.1 38.6 + - - +
73C GLU* 1.3 76.3 - - - +
75C ASN* 1.3 61.9 + - - +
76C ASP 3.3 0.2 + - - -
77C MET* 3.4 2.8 + - - +
78C LEU* 3.1 35.7 + - + +
90C LEU* 3.1 46.3 + - + +
93C GLN* 3.4 31.8 - - - +
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Residues in contact with ASN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A LYS* 5.8 0.4 - - - +
445A LYS* 4.6 13.4 + - - -
71C THR 3.2 18.9 + - - +
72C ASP* 3.3 20.8 + - - +
74C GLU* 1.3 79.7 - - - +
76C ASP* 1.3 59.3 + - - +
78C LEU* 3.4 11.8 + - - +
79C ASP* 3.0 39.3 + - - +
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Residues in contact with ASP 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A LYS* 2.7 39.1 + - - +
452A ASN* 4.2 9.6 + - - +
465A ARG* 4.2 17.4 + - - +
466A ARG* 4.7 2.8 + - - +
469A GLU* 4.3 14.6 - - - +
72C ASP 3.0 19.4 - - - +
73C GLU* 3.4 15.2 + - - +
74C GLU 3.2 0.2 - - - -
75C ASN* 1.3 74.2 - - - +
77C MET* 1.3 70.3 + - + +
78C LEU 3.1 2.5 + - - -
79C ASP* 3.5 14.6 + - - +
80C LEU* 3.9 17.2 - - - +
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Residues in contact with MET 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A TRP* 6.4 1.6 - - - -
458A GLY 6.0 2.9 - - - +
461A GLN* 3.9 13.5 - - - +
465A ARG* 3.4 32.3 - - - +
466A ARG* 5.3 5.4 - - - +
50C LEU* 3.8 23.6 - - + +
52C CYS* 3.4 42.0 - - - +
53C SER* 3.4 13.5 + - - -
73C GLU 3.3 13.6 + - - +
74C GLU 3.4 7.1 + - - +
76C ASP* 1.3 81.6 - - + +
78C LEU* 1.3 59.2 + - - +
80C LEU* 3.4 32.4 + - + +
81C ALA* 5.4 0.2 - - - +
90C LEU* 3.8 12.6 - - + -
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A LYS* 6.4 0.2 - - - +
53C SER* 5.6 1.6 - - - -
74C GLU* 3.1 25.8 + - + +
75C ASN* 3.7 13.2 - - - +
76C ASP 3.1 0.2 - - - -
77C MET* 1.3 76.1 - - - +
79C ASP* 1.3 56.6 + - - +
80C LEU 2.8 15.8 + - - -
81C ALA* 3.6 21.3 - - + +
90C LEU* 3.6 43.1 - - + +
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A LYS* 5.0 5.2 + - - -
440A TRP 5.7 0.9 - - - +
445A LYS* 4.0 29.0 + - - +
448A THR* 4.0 28.0 + - - +
449A TYR* 4.0 11.2 - - - -
450A PHE 3.6 12.0 + - - -
452A ASN* 6.3 2.9 - - + -
75C ASN* 3.0 23.8 + - - +
76C ASP* 3.5 10.7 + - - +
78C LEU* 1.3 76.2 - - - +
80C LEU* 1.3 68.9 + - + +
81C ALA 3.9 1.1 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il